I believe you can specifically set within the idecomp portion, a flag
saying which residues you want to consider specifically (I think it's in
the manual or in some example in the manual). This will of course require
you to know which residues you expect to participate in binding.
~Aron
On Sun, Dec 9, 2012 at 1:08 AM, dbaogen <dbaogen.gmail.com> wrote:
> Dear all,
>
> In the calculation of binding free energy between
> protein-ligand, if I want to know the interaction energy between ligand and
> the residues within a specific distance around it, how should I set the
> parameters in the input files? According to the instructions in manual, the
> 'idecomp' parameter will seem to give every pairwise interaction energy
> between residues in the studied system. This will cost a lot of
> computational time to the large system. Would you like to give me some
> suggestions about interaction energy calculation only considering ligand
> and its neighbor residues? Thank you!
>
> Best wishes,
>
> Duan Baogen
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sun Dec 09 2012 - 00:00:02 PST
